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Some information such as custom columns is library specific and therefore stored in the metadata.db file for that particular library. Not sure why that would not have come across when you copied the library folder.
Other information is user specific. When you have Calibre portable running, did you go into Preferences to check where it is looking for settings so that you copied the settings to that location.
Having said that I believe that there can be problems with some plugins which store absolute path information in the preferences.
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